Source code for graph_tool.draw.graphviz_draw

#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# graph_tool -- a general graph manipulation python module
#
# Copyright (C) 2006-2017 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

from __future__ import division, absolute_import, print_function

import sys
if sys.version_info < (3,):
    range = xrange
else:
    unicode = str
import os
import os.path
import time
import warnings
import ctypes
import ctypes.util
import tempfile
from .. import PropertyMap, group_vector_property, ungroup_vector_property, _c_str
import numpy
import numpy.random
import copy

from .. draw import arf_layout

try:
    import matplotlib.cm
    import matplotlib.colors
except ImportError:
    msg = "Error importing matplotlib module... graphviz_draw() will not work"
    warnings.filterwarnings("always", msg, ImportWarning)
    warnings.warn(msg, ImportWarning)
    raise

try:
    libname = ctypes.util.find_library("c")
    libc = ctypes.CDLL(libname)
    if hasattr(libc, "open_memstream"):
        libc.open_memstream.restype = ctypes.POINTER(ctypes.c_char)
except OSError:
    msg = "Error importing C standard library... graphviz_draw() will not work."
    warnings.filterwarnings("always", msg, ImportWarning)
    warnings.warn(msg, ImportWarning)
    pass


try:
    libname = ctypes.util.find_library("gvc")
    if libname is None:
        raise OSError()
    libgv = ctypes.CDLL(libname, ctypes.RTLD_GLOBAL)
    # properly set the return types of certain functions
    ptype = ctypes.POINTER(ctypes.c_char)
    libgv.gvContext.restype = ptype
    libgv.agopen.restype = ptype
    libgv.agnode.restype = ptype
    libgv.agedge.restype = ptype
    libgv.agget.restype = ptype
    libgv.agstrdup_html.restype = ptype
    # create a context to use the whole time (if we keep freeing and recreating
    # it, we will hit a memory leak in graphviz)
    gvc = libgv.gvContext()

    try:
        gv_new_api = True
        libgv_directed = libgv.Agdirected
        libgv_undirected = libgv.Agundirected
    except AttributeError:
        gv_new_api = False
        libgv_directed = 1
        libgv_undirected = 0

except OSError:
    msg = "Error importing graphviz C library (libgvc)... graphviz_draw() will not work."
    warnings.filterwarnings("always", msg, ImportWarning)
    warnings.warn(msg, ImportWarning)


def htmlize(val):
    if len(val) >= 2 and val[0] == "<" and val[-1] == ">":
        return ctypes.string_at(libgv.agstrdup_html(val[1:-1]))
    return val


def aset(elem, attr, value):
    v = htmlize(str(value)).encode("utf8")
    libgv.agsafeset(elem, str(attr).encode("utf8"), v, v)


def aget(elem, attr):
    s = ctypes.string_at(libgv.agget(elem,
                                     str(attr).encode("utf8")))
    return s.decode("utf8")


[docs]def graphviz_draw(g, pos=None, size=(15, 15), pin=False, layout=None, maxiter=None, ratio="fill", overlap=True, sep=None, splines=False, vsize=0.105, penwidth=1.0, elen=None, gprops={}, vprops={}, eprops={}, vcolor="#a40000", ecolor="#2e3436", vcmap=None, vnorm=True, ecmap=None, enorm=True, vorder=None, eorder=None, output="", output_format="auto", fork=False, return_string=False): r"""Draw a graph using graphviz. Parameters ---------- g : :class:`~graph_tool.Graph` Graph to be drawn. pos : :class:`~graph_tool.PropertyMap` or tuple of :class:`~graph_tool.PropertyMap` (optional, default: ``None``) Vertex property maps containing the x and y coordinates of the vertices. size : tuple of scalars (optional, default: ``(15,15)``) Size (in centimeters) of the canvas. pin : bool or :class:`~graph_tool.PropertyMap` (default: ``False``) If ``True``, the vertices are not moved from their initial position. If a :class:`~graph_tool.PropertyMap` is passed, it is used to pin nodes individually. layout : string (default: ``"neato" if g.num_vertices() <= 1000 else "sfdp"``) Layout engine to be used. Possible values are ``"neato"``, ``"fdp"``, ``"dot"``, ``"circo"``, ``"twopi"`` and ``"arf"``. maxiter : int (default: ``None``) If specified, limits the maximum number of iterations. ratio : string or float (default: ``"fill"``) Sets the aspect ratio (drawing height/drawing width) for the drawing. Note that this is adjusted before the ``size`` attribute constraints are enforced. If ``ratio`` is numeric, it is taken as the desired aspect ratio. Then, if the actual aspect ratio is less than the desired ratio, the drawing height is scaled up to achieve the desired ratio; if the actual ratio is greater than that desired ratio, the drawing width is scaled up. If ``ratio == "fill"`` and the size attribute is set, node positions are scaled, separately in both x and y, so that the final drawing exactly fills the specified size. If ``ratio == "compress"`` and the size attribute is set, dot attempts to compress the initial layout to fit in the given size. This achieves a tighter packing of nodes but reduces the balance and symmetry. This feature only works in dot. If ``ratio == "expand"``, the size attribute is set, and both the width and the height of the graph are less than the value in size, node positions are scaled uniformly until at least one dimension fits size exactly. Note that this is distinct from using size as the desired size, as here the drawing is expanded before edges are generated and all node and text sizes remain unchanged. If ``ratio == "auto"``, the page attribute is set and the graph cannot be drawn on a single page, then size is set to an "ideal" value. In particular, the size in a given dimension will be the smallest integral multiple of the page size in that dimension which is at least half the current size. The two dimensions are then scaled independently to the new size. This feature only works in dot. overlap : bool or string (default: ``"prism"``) Determines if and how node overlaps should be removed. Nodes are first enlarged using the sep attribute. If ``True``, overlaps are retained. If the value is ``"scale"``, overlaps are removed by uniformly scaling in x and y. If the value is ``False``, node overlaps are removed by a Voronoi-based technique. If the value is ``"scalexy"``, x and y are separately scaled to remove overlaps. If sfdp is available, one can set overlap to ``"prism"`` to use a proximity graph-based algorithm for overlap removal. This is the preferred technique, though ``"scale"`` and ``False`` can work well with small graphs. This technique starts with a small scaling up, controlled by the overlap_scaling attribute, which can remove a significant portion of the overlap. The prism option also accepts an optional non-negative integer suffix. This can be used to control the number of attempts made at overlap removal. By default, ``overlap == "prism"`` is equivalent to ``overlap == "prism1000"``. Setting ``overlap == "prism0"`` causes only the scaling phase to be run. If the value is ``"compress"``, the layout will be scaled down as much as possible without introducing any overlaps, obviously assuming there are none to begin with. sep : float (default: ``None``) Specifies margin to leave around nodes when removing node overlap. This guarantees a minimal non-zero distance between nodes. splines : bool (default: ``False``) If ``True``, the edges are drawn as splines and routed around the vertices. vsize : float, :class:`~graph_tool.PropertyMap`, or tuple (default: ``0.105``) Default vertex size (width and height). If a tuple is specified, the first value should be a property map, and the second is a scale factor. penwidth : float, :class:`~graph_tool.PropertyMap` or tuple (default: ``1.0``) Specifies the width of the pen, in points, used to draw lines and curves, including the boundaries of edges and clusters. It has no effect on text. If a tuple is specified, the first value should be a property map, and the second is a scale factor. elen : float or :class:`~graph_tool.PropertyMap` (default: ``None``) Preferred edge length, in inches. gprops : dict (default: ``{}``) Additional graph properties, as a dictionary. The keys are the property names, and the values must be convertible to string. vprops : dict (default: ``{}``) Additional vertex properties, as a dictionary. The keys are the property names, and the values must be convertible to string, or vertex property maps, with values convertible to strings. eprops : dict (default: ``{}``) Additional edge properties, as a dictionary. The keys are the property names, and the values must be convertible to string, or edge property maps, with values convertible to strings. vcolor : string or :class:`~graph_tool.PropertyMap` (default: ``"#a40000"``) Drawing color for vertices. If the valued supplied is a property map, the values must be scalar types, whose color values are obtained from the ``vcmap`` argument. ecolor : string or :class:`~graph_tool.PropertyMap` (default: ``"#2e3436"``) Drawing color for edges. If the valued supplied is a property map, the values must be scalar types, whose color values are obtained from the ``ecmap`` argument. vcmap : :class:`matplotlib.colors.Colormap` (default: :class:`matplotlib.cm.jet`) Vertex color map. vnorm : bool (default: ``True``) Normalize vertex color values to the [0,1] range. ecmap : :class:`matplotlib.colors.Colormap` (default: :class:`matplotlib.cm.jet`) Edge color map. enorm : bool (default: ``True``) Normalize edge color values to the [0,1] range. vorder : :class:`~graph_tool.PropertyMap` (default: ``None``) Scalar vertex property map which specifies the order with which vertices are drawn. eorder : :class:`~graph_tool.PropertyMap` (default: ``None``) Scalar edge property map which specifies the order with which edges are drawn. output : string (default: ``""``) Output file name. output_format : string (default: ``"auto"``) Output file format. Possible values are ``"auto"``, ``"xlib"``, ``"ps"``, ``"svg"``, ``"svgz"``, ``"fig"``, ``"mif"``, ``"hpgl"``, ``"pcl"``, ``"png"``, ``"gif"``, ``"dia"``, ``"imap"``, ``"cmapx"``. If the value is ``"auto"``, the format is guessed from the ``output`` parameter, or ``xlib`` if it is empty. If the value is ``None``, no output is produced. fork : bool (default: ``False``) If ``True``, the program is forked before drawing. This is used as a work-around for a bug in graphviz, where the ``exit()`` function is called, which would cause the calling program to end. This is always assumed ``True``, if ``output_format == 'xlib'``. return_string : bool (default: ``False``) If ``True``, a string containing the rendered graph as binary data is returned (defaults to png format). Returns ------- pos : :class:`~graph_tool.PropertyMap` Vector vertex property map with the x and y coordinates of the vertices. gv : gv.digraph or gv.graph (optional, only if ``returngv == True``) Internally used graphviz graph. Notes ----- This function is a wrapper for the [graphviz]_ routines. Extensive additional documentation for the graph, vertex and edge properties is available at: http://www.graphviz.org/doc/info/attrs.html. Examples -------- .. testcode:: :hide: np.random.seed(42) gt.seed_rng(42) from numpy import sqrt >>> g = gt.price_network(1500) >>> deg = g.degree_property_map("in") >>> deg.a = 2 * (sqrt(deg.a) * 0.5 + 0.4) >>> ebet = gt.betweenness(g)[1] >>> gt.graphviz_draw(g, vcolor=deg, vorder=deg, elen=10, ... ecolor=ebet, eorder=ebet, output="graphviz-draw.pdf") <...> .. testcode:: :hide: gt.graphviz_draw(g, vcolor=deg, vorder=deg, elen=10, ecolor=ebet, eorder=ebet, output="graphviz-draw.png") .. figure:: graphviz-draw.* :align: center Kamada-Kawai force-directed layout of a Price network with 1500 nodes. The vertex size and color indicate the degree, and the edge color corresponds to the edge betweenness centrality References ---------- .. [graphviz] http://www.graphviz.org """ if output != "" and output is not None: output = os.path.expanduser(output) # check opening file for writing, since graphviz will bork if it is not # possible to open file if os.path.dirname(output) != "" and \ not os.access(os.path.dirname(output), os.W_OK): raise IOError("cannot write to " + os.path.dirname(output)) has_layout = False try: if gv_new_api: gvg = libgv.agopen("G".encode("utf8"), libgv_directed if g.is_directed() else libgv_undirected, 0) else: gvg = libgv.agopen("G".encode("utf8"), libgv_directed if g.is_directed() else libgv_undirected) if layout is None: if pin == False: layout = "neato" if g.num_vertices() <= 1000 else "sfdp" else: layout = "neato" if layout == "arf": layout = "neato" pos = arf_layout(g, pos=pos) pin = True if pos is not None: # copy user-supplied property if isinstance(pos, PropertyMap): pos = ungroup_vector_property(pos, [0, 1]) else: pos = (g.copy_property(pos[0]), g.copy_property(pos[1])) if type(vsize) == tuple: s = g.new_vertex_property("double") g.copy_property(vsize[0], s) s.a *= vsize[1] vsize = s if type(penwidth) == tuple: s = g.new_edge_property("double") g.copy_property(penwidth[0], s) s.a *= penwidth[1] penwidth = s # main graph properties aset(gvg, "outputorder", "edgesfirst") aset(gvg, "mode", "major") if type(overlap) is bool: overlap = "true" if overlap else "false" else: overlap = str(overlap) aset(gvg, "overlap", overlap) if sep is not None: aset(gvg, "sep", sep) if splines: aset(gvg, "splines", "true") aset(gvg, "ratio", ratio) # size is in centimeters... convert to inches aset(gvg, "size", "%f,%f" % (size[0] / 2.54, size[1] / 2.54)) if maxiter is not None: aset(gvg, "maxiter", maxiter) seed = numpy.random.randint(sys.maxsize) aset(gvg, "start", "%d" % seed) # apply all user supplied graph properties for k, val in gprops.items(): if isinstance(val, PropertyMap): aset(gvg, k, val[g]) else: aset(gvg, k, val) # normalize color properties if (isinstance(vcolor, PropertyMap) and vcolor.value_type() != "string"): minmax = [numpy.inf, -numpy.inf] for v in g.vertices(): c = vcolor[v] minmax[0] = min(c, minmax[0]) minmax[1] = max(c, minmax[1]) if minmax[0] == minmax[1]: minmax[1] += 1 if vnorm: vnorm = matplotlib.colors.Normalize(vmin=minmax[0], vmax=minmax[1]) else: vnorm = lambda x: x if (isinstance(ecolor, PropertyMap) and ecolor.value_type() != "string"): minmax = [numpy.inf, -numpy.inf] for e in g.edges(): c = ecolor[e] minmax[0] = min(c, minmax[0]) minmax[1] = max(c, minmax[1]) if minmax[0] == minmax[1]: minmax[1] += 1 if enorm: enorm = matplotlib.colors.Normalize(vmin=minmax[0], vmax=minmax[1]) else: enorm = lambda x: x if vcmap is None: vcmap = matplotlib.cm.jet if ecmap is None: ecmap = matplotlib.cm.jet # add nodes if vorder is not None: vertices = sorted(g.vertices(), key = lambda a: vorder[a]) else: vertices = g.vertices() for v in vertices: if gv_new_api: n = libgv.agnode(gvg, str(int(v)).encode("utf8"), 1) else: n = libgv.agnode(gvg, str(int(v)).encode("utf8")) if type(vsize) == PropertyMap: vw = vh = vsize[v] else: vw = vh = vsize aset(n, "shape", "circle") aset(n, "width", "%g" % vw) aset(n, "height", "%g" % vh) aset(n, "style", "filled") aset(n, "color", "#2e3436") # apply color if isinstance(vcolor, (str, unicode)): aset(n, "fillcolor", _c_str(vcolor)) else: color = vcolor[v] if isinstance(color, (str, unicode)): aset(n, "fillcolor", _c_str(color)) else: color = tuple([int(c * 255.0) for c in vcmap(vnorm(color))]) aset(n, "fillcolor", "#%.2x%.2x%.2x%.2x" % color) aset(n, "label", "") # user supplied position if pos is not None: if isinstance(pin, bool): pin_val = pin else: pin_val = pin[v] aset(n, "pos", "%f,%f%s" % (pos[0][v], pos[1][v], "!" if pin_val else "")) aset(n, "pin", pin_val) # apply all user supplied properties for k, val in vprops.items(): if isinstance(val, PropertyMap): aset(n, k, val[v]) else: aset(n, k, val) # add edges if eorder is not None: edges = sorted(g.edges(), key = lambda a: eorder[a]) else: edges = g.edges() for e in edges: if gv_new_api: ge = libgv.agedge(gvg, libgv.agnode(gvg, str(int(e.source())).encode("utf8"), False), libgv.agnode(gvg, str(int(e.target())).encode("utf8"), False), str(g.edge_index[e]).encode("utf8"), 1) else: ge = libgv.agedge(gvg, libgv.agnode(gvg, str(int(e.source())).encode("utf8")), libgv.agnode(gvg, str(int(e.target())).encode("utf8"))) aset(ge, "arrowsize", "0.3") if g.is_directed(): aset(ge, "arrowhead", "vee") aset(ge, "dir", "forward") else: aset(ge, "dir", "none") # apply color if isinstance(ecolor, (str, unicode)): aset(ge, "color", _c_str(ecolor)) else: color = ecolor[e] if isinstance(color, (str, unicode)): aset(ge, "color", _c_str(color)) else: color = tuple([int(c * 255.0) for c in ecmap(enorm(color))]) aset(ge, "color", "#%.2x%.2x%.2x%.2x" % color) # apply edge length if elen is not None: if isinstance(elen, PropertyMap): aset(ge, "len", elen[e]) else: aset(ge, "len", elen) # apply width if penwidth is not None: if isinstance(penwidth, PropertyMap): aset(ge, "penwidth", penwidth[e]) else: aset(ge, "penwidth", penwidth) # apply all user supplied properties for k, v in eprops.items(): if isinstance(v, PropertyMap): aset(ge, k, v[e]) else: aset(ge, k, v) libgv.gvLayout(gvc, gvg, layout.encode("utf8")) has_layout = True retv = libgv.gvRender(gvc, gvg, "dot".encode("utf8"), None) # retrieve positions only if pos is None: pos = (g.new_vertex_property("double"), g.new_vertex_property("double")) for v in g.vertices(): n = libgv.agnode(gvg, str(int(v)).encode("utf8")) p = aget(n, "pos") p = p.split(",") pos[0][v] = float(p[0]) pos[1][v] = float(p[1]) # I don't get this, but it seems necessary pos[0].a /= 100 pos[1].a /= 100 pos = group_vector_property(pos) if return_string: if output_format == "auto": output_format = "png" if hasattr(libc, "open_memstream"): buf = ctypes.c_char_p() buf_len = ctypes.c_size_t() fstream = libc.open_memstream(ctypes.byref(buf), ctypes.byref(buf_len)) libgv.gvRender(gvc, gvg, output_format.encode("utf8"), fstream) libc.fclose(fstream) data = copy.copy(ctypes.string_at(buf, buf_len.value)) libc.free(buf) else: # write to temporary file, if open_memstream is not available output = tempfile.mkstemp()[1] libgv.gvRenderFilename(gvc, gvg, output_format.encode("utf8"), output.encode("utf8")) data = open(output).read() os.remove(output) else: if output_format == "auto": if output == "": output_format = "xlib" elif output is not None: output_format = output.split(".")[-1] # if using xlib we need to fork the process, otherwise good ol' # graphviz will call exit() when the window is closed if output_format == "xlib" or fork: pid = os.fork() if pid == 0: libgv.gvRenderFilename(gvc, gvg, output_format.encode("utf8"), output.encode("utf8")) os._exit(0) # since we forked, it's good to be sure if output_format != "xlib": os.wait() elif output is not None: libgv.gvRenderFilename(gvc, gvg, output_format.encode("utf8"), output.encode("utf8")) ret = [pos] if return_string: ret.append(data) finally: if has_layout: libgv.gvFreeLayout(gvc, gvg) libgv.agclose(gvg) if len(ret) > 1: return tuple(ret) else: return ret[0]